George McNamara comments on spectra viewers
Posted On: Sunday, February 15, 2015
The material below was submitted by George McNamara, MD Anderson Cancer Center, as a comment on our spectra viewer blog post. George has been a strong advocate for increased public access to spectral data and a pioneer in accumulating such data and making it available. Because of the length and the value of his contribution we are publishing it as its own post.
From George McNamara:
Much of the older (2006 and earlier) data used in the graphing spectra viewers is in an Excel XLSX file in the PubSpectra download zip at http://works.bepress.com/gmcnamara/9/
In turn, McNamara et al 2006 Cytometry, provides the sources of the data in the Excel file (many from Molecular Probes, not Invitrogen/LifeTech/ThermoFisher, many FP’s from Roger Tsien and Robert Campbell – the Excel file cites the source of EVERY spectra trace),
http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.20304/abstract
(open access – much of the paper was about the precursor to the current UA web site).
The sources of the PubSpectra data are also summarized in a table in the middle of http://home.earthlink.net/~pubspectra/. The top part of that page has my original posters on Tattletales & T-Bow, my concept to multiplex FP’s, FP biosensors, and/or bioluminescent proteins — see Saito … Nagai 2012 for Nano-Lanterns (open access). We still have not made any Tattletales or T-Bows in our lab (which may be just as well, our thinking has evolved in the past ~2.5 years since conception). My current thinking — and references of others making TALE-FPs, Cas9-FPs, etc,, is available for download at http://works.bepress/gmcnamara/65/.
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I currently mostly use Semrock‘s web site, occasionally Chroma‘s.
Additional spectra web sites include:
Leica FluoScout™ (limited, but may be useful to Leica customers)
Zeiss ZEN and Leica LAS AF confocal microscope software (not necessarily the free versions) includes spectra viewers to help set instrument parameters. The ZEN 1.0 software used – and credited – the Pubspectra data set. Zeiss has an iThingy app that uses PubSpectra data.
The confocal Listserv occasionally has sweeps of spectra data and viewers, such as this one
Not spectra (so far) – I find very useful Kurt Thorn’s Fluorescent protein properties web page with interactive scatter plots (try [photo]Stability vs Brightness)
Requests:
* when publishing, it would be great if authors would include numerical data – preferably as an Excel file that matches the PubSpectra format – as a supplemental file.
* Reviewers and editors should INSIST that authors provide all their biomedical fluorescence spectra as numerical data, in addition to ‘dead end” graphs.
* I would love to see someone ‘convert’ the PubSpectra data — and supplement by pulling out all the newer spectra data from SearchLight etc, into Tableau Public or a similar online graphing program – ideally with a way to add more data.
* I have additional comments/suggestions posted at
http://works.bepress.com/gmcnamara/50/
Lastly, most researchers are still using EGFP — this is 1996 technology. Are you still driving a 1996 car, using a 1996 cell phone, 1996 computer, or 1996 microscope? Current generation GFP’s are more than 3x brighter than EGFP. See http://works.bepress.com/gmcnamara/63/ for a list of possible current generation colors, along with Kurt Thorn’s FP Properties web page (see above), and the references in http://works.bepress.com/gmcnamara/65
George McNamara
M.D. Anderson Cancer Center
Houston, TX